We had a sharp-eyed researcher notice that her tophat output with various parameters was always yielding the same results. JJ tracked it down to a bug in tophat_wrapper.py where the segment-length and segment-mismatches are displayed in the options and are parsed in ophat_wrapper.py, but those options are never added to the actual command line for tophat.
Attached is a patch that wires them up.
Included in galaxy-central changeset 4501:0b278c24c19f
Thanks!
On Oct 27, 2010, at 5:51 PM, Ry4an Brase wrote:
We had a sharp-eyed researcher notice that her tophat output with various parameters was always yielding the same results. JJ tracked it down to a bug in tophat_wrapper.py where the segment-length and segment-mismatches are displayed in the options and are parsed in ophat_wrapper.py, but those options are never added to the actual command line for tophat.
Attached is a patch that wires them up.
-- Ry4an Brase 612-626-6575 Software Developer Application Development University of Minnesota Supercomputing Institute http://www.msi.umn.edu <jj-fix-tophat.patch>_______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
J.
galaxy-dev@lists.galaxyproject.org
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Jeremy Goecks -
Ry4an Brase